You can't make her commit to you, the marriage or your family and in reality the harder you try the more you'll push her in the wrong direction. Weird I know, but this is how the mind of a cheater works.
The only chance you have is to force her to realize that you will not accept her behavior, that you will not be a part of a three person marriage, that she cannot have her cake and eat it to. The hard part is that to get her to realize it you have to mean it, and there is no guarantee that in forcing her to this realization she will pick you and the marriage. If she doesn't you have to be prepared to move on.
Just off the cuff it sounds like you're battling two issues. One is her affair fogged mind, treat this like you would if you were trying to break her of a drug addiction and the OM is the drug - literally. The second, and this one is just a hunch, is possibly a little bit of nice guy syndrome; doing too much to try to please her, to meet her needs, to get her to stay - all at the expense of you. Hop over to the Men's Clubhouse and do a little reading on it and see if it hit close to home - or download the book, No More Mr. Nice Guy. Just a hunch and I maybe off base on this one.
Good Luck - remember you can't make her do or choose anything. All you can do is decide what you will and won't accept and how you will react accordingly and make sure she knows this.